Corrected readme and added files

20191015_Brief introduction to R_Proj_AM.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

README.Rmd

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+---
+title: "README"
+date: "`r format(Sys.time(), '%d %B %Y')`"
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+
+# Brief introduction to R for Epidemiologists
+
+### Background:
+
+This repository is for the development and maintenance of R teaching material for use in the EPIET (European Programme of Intervention Epidemiology Training) and UK FETP (United Kingdom Field Epidemiology Training Programme) **introductory course (IC)**.
+
+The module now includes a brief demonstration session to introduce participants to R.  
+
+An R markdown document demonstrates how to perform key tasks for epidemiologists:
+
+ - Setting up an R project file in RStudio
+ - Create an R script
+ - Create an R markdown / notebook file
+ - Installing and loading packages
+ - Setting the working directory using the `here` package
+ - Importing and viewing a dataset
+ - Exploring an imported dataset
+ - Recoding variables
+ - Creating new variables with conditional logic (e.g. a case definition)
+ - Performing descriptive analysis (epicurve of symptom onset dates and age sex profile of cases)
+ - Calculating risk ratios for exposures (raw and stratified)
+
+
+### Acknowledgements:
+
+This material is based on an equivalent introductory guide to STATA for epidemiologists, written by Alicia Barrasa, for the EPIET/EUPHEM programme introductory course.  The document demonstrates how to perform the same steps in R.
+
+
+### Requirements:
+
+This demonstration uses a STATA `.dta` teaching dataset from an outbreak of gastrointestinal infection that occured at a school dinner.  The dataset is included in this repository.
+
+To run this demonstration, the demonstrator will need the following software installed on their machine:
+
+ - R (download and install the latest version from CRAN [here](https://cran.r-project.org/))
+ - RStudio (download the latest version as an installer or ready-to-use `.zip` file [here](https://rstudio.com/products/rstudio/download/))
+ - Rtools (download and install the latest version from CRAN [here](https://cran.r-project.org/bin/windows/Rtools/))
+
+
+In addition, the following packages are required (the first chunk in the R markdown document will automatically install them if needed when run on the demonstrator's machine):
+
+ - `here`: locates your working directory in the folder where you created your `.Rproj` file
+ - `haven`: imports STATA `.dta` datasets and other less common file types into R
+ - `data.table`: data cleaning, recoding, reshaping and creating summary tables 
+ - `lubridate`: performing calculations with dates
+ - `epitrix`: create 2x2 epitables and other functions for cleaning epidemiological data
+ - `ggplot2`: create graphs
+ - `epitools`: calculate risk ratios
+ - `EpiFunc`: create descriptive epidemiology figures (age sex pyramids and epicurves)
+ - `devtools`: used to install and build the `EpiFunc` package from Github 
+
+
+### How to use:
+
+After installing the above software, clone this repository either by clicking on the green `Clone or download` button on this page, or by entering the following command into git bash:
+
+```{r, eval=FALSE}
+
+git clone https://github.com/EPIET/IntroductoryCourse.git
+
+```
+
+
+Then:
+
+ - Open the .Rproj file in RStudio
+ - Navigate to the `Files` tab within RStudio 
+ - Click on `20191015_Brief introduction to R_script_AM.Rmd` R markdown document to open it
+ - Run each chunk separately in the live demonstration, explaining what is happening as you go.
+
+To provide a printed copy of the demonstration R markdown for participants:
+
+ - Open the R markdown document in RStudio (as above)
+ - Click on the `Knit` button and select `Knit to pdf`
+ - This will save a .pdf version of the document in your working directory, which can then be printed.
+
+
+### Maintenance:
+
+This project is currently being maintained by [Amy Mikhail](https://github.com/AmyMikhail).  
+
+Contributions are welcome: please contact the maintainer to request access.
+
+To report bugs or make feature requests, please post an issue [here](https://github.com/EPIET/IntroductoryCourse/issues).

README.md

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+README
+================
+20 November 2019
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# Brief introduction to R for Epidemiologists
+
+### Background:
+
+This repository is for the development and maintenance of R teaching
+material for use in the EPIET (European Programme of Intervention
+Epidemiology Training) and UK FETP (United Kingdom Field Epidemiology
+Training Programme) **introductory course (IC)**.
+
+The module now includes a brief demonstration session to introduce
+participants to R.
+
+An R markdown document demonstrates how to perform key tasks for
+epidemiologists:
+
+  - Setting up an R project file in RStudio
+  - Create an R script
+  - Create an R markdown / notebook file
+  - Installing and loading packages
+  - Setting the working directory using the `here` package
+  - Importing and viewing a dataset
+  - Exploring an imported dataset
+  - Recoding variables
+  - Creating new variables with conditional logic (e.g. a case
+    definition)
+  - Performing descriptive analysis (epicurve of symptom onset dates and
+    age sex profile of cases)
+  - Calculating risk ratios for exposures (raw and stratified)
+
+### Acknowledgements:
+
+This material is based on an equivalent introductory guide to STATA for
+epidemiologists, written by Alicia Barrasa, for the EPIET/EUPHEM
+programme introductory course. The document demonstrates how to perform
+the same steps in R.
+
+### Requirements:
+
+This demonstration uses a STATA `.dta` teaching dataset from an outbreak
+of gastrointestinal infection that occured at a school dinner. The
+dataset is included in this repository.
+
+To run this demonstration, the demonstrator will need the following
+software installed on their machine:
+
+  - R (download and install the latest version from CRAN
+    [here](https://cran.r-project.org/))
+  - RStudio (download the latest version as an installer or ready-to-use
+    `.zip` file [here](https://rstudio.com/products/rstudio/download/))
+  - Rtools (download and install the latest version from CRAN
+    [here](https://cran.r-project.org/bin/windows/Rtools/))
+
+In addition, the following packages are required (the first chunk in the
+R markdown document will automatically install them if needed when run
+on the demonstrator’s machine):
+
+  - `here`: locates your working directory in the folder where you
+    created your `.Rproj` file
+  - `haven`: imports STATA `.dta` datasets and other less common file
+    types into R
+  - `data.table`: data cleaning, recoding, reshaping and creating
+    summary tables
+  - `lubridate`: performing calculations with dates
+  - `epitrix`: create 2x2 epitables and other functions for cleaning
+    epidemiological data
+  - `ggplot2`: create graphs
+  - `epitools`: calculate risk ratios
+  - `EpiFunc`: create descriptive epidemiology figures (age sex pyramids
+    and epicurves)
+  - `devtools`: used to install and build the `EpiFunc` package from
+    Github
+
+### How to use:
+
+After installing the above software, clone this repository either by
+clicking on the green `Clone or download` button on this page, or by
+entering the following command into git bash:
+
+``` r
+
+git clone https://github.com/EPIET/IntroductoryCourse.git
+```
+
+Then:
+
+  - Open the .Rproj file in RStudio
+  - Navigate to the `Files` tab within RStudio
+  - Click on `20191015_Brief introduction to R_script_AM.Rmd` R markdown
+    document to open it
+  - Run each chunk separately in the live demonstration, explaining what
+    is happening as you go.
+
+To provide a printed copy of the demonstration R markdown for
+participants:
+
+  - Open the R markdown document in RStudio (as above)
+  - Click on the `Knit` button and select `Knit to pdf`
+  - This will save a .pdf version of the document in your working
+    directory, which can then be printed.
+
+### Maintenance:
+
+This project is currently being maintained by [Amy
+Mikhail](https://github.com/AmyMikhail).
+
+Contributions are welcome: please contact the maintainer to request
+access.
+
+To report bugs or make feature requests, please post an issue
+[here](https://github.com/EPIET/IntroductoryCourse/issues).